Merge pull request #61 from sanger-tol/mm49_main

Major tidy up of the repository and the website

.github/CONTRIBUTING.md

@@ -7,7 +7,7 @@ Hi there! Many thanks for taking an interest in improving the sanger-tol website
 If you'd like to write some code for sanger-tol/pipelines-website, the standard workflow is as follows:
 
 1. Check that there isn't already an issue about your idea in the
- [sanger-tol/pipelines-website issues](<[https://github.com/nf-core/nf-co.re/issues](https://github.com/sanger-tol/pipelines-website/issues)>) to avoid duplicating work.
+ [sanger-tol/pipelines-website issues](https://github.com/sanger-tol/pipelines-website/issues) to avoid duplicating work.
  - If there isn't one already, please create one so that others know you're working on this
 2. Fork the [sanger-tol/pipelines-website repository](https://github.com/sanger-tol/pipelines-website) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
@@ -23,4 +23,4 @@ For now, the only test is for Markdown syntax, using the `markdownlint` package.
 
 ## Getting help
 
-For further information or help, please [contact us](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=priyanka-surana%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
+For further information or help, please [contact us](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).

.github/ISSUE_TEMPLATE/add_team.yaml

@@ -3,7 +3,7 @@ description: Add details to include your team details to the website
 title: '[Team]: '
 labels: ['team', 'enhancement']
 assignees:
- - priyanka-surana
+ - muffato
 body:
  - type: markdown
  attributes:

.github/ISSUE_TEMPLATE/add_team_members.yaml

@@ -3,7 +3,7 @@ description: Add your details to the team page on the website
 title: '[Team member]: '
 labels: ['team', 'enhancement']
 assignees:
- - priyanka-surana
+ - muffato
 body:
  - type: markdown
  attributes:

.github/ISSUE_TEMPLATE/add_team_projects.yaml

@@ -3,7 +3,7 @@ description: Add project details to include in team page on the website
 title: '[Project]: '
 labels: ['team', 'enhancement']
 assignees:
- - priyanka-surana
+ - muffato
 body:
  - type: markdown
  attributes:

.github/ISSUE_TEMPLATE/add_tool.yaml

@@ -3,7 +3,7 @@ description: Add details to include your tool to the website
 title: '[Tool]: '
 labels: ['tool', 'enhancement']
 assignees:
- - priyanka-surana
+ - muffato
 body:
  - type: markdown
  attributes:

.github/ISSUE_TEMPLATE/contact_us.yaml

@@ -3,7 +3,6 @@ description: Get in touch with the Tree of Life informatics teams.
 title: '[Contact Us]: '
 labels: ['connect']
 assignees:
- - priyanka-surana
  - muffato
 body:
  - type: markdown

.github/ISSUE_TEMPLATE/publications.yaml

@@ -2,7 +2,7 @@ name: Add publications
 description: Add publication to the sanger-tol website
 title: '[Publication]: DOI'
 assignees:
- - priyanka-surana
+ - muffato
 body:
  - type: markdown
  attributes:

.prettierignore

@@ -19,7 +19,6 @@ public_html/tools/docs/
 nfcore_stats.json
 nfcore_issue_stats.json
 markdown/pipelines
-markdown/tools
 api_cache
 contributor_stats
 update.log
@@ -43,4 +42,4 @@ php.ini
 node_modules
 vendor
 backstop_data
-.mysql-data/
+.mysql-data/

CODE_OF_CONDUCT.md

@@ -50,7 +50,7 @@ Members of the Safety Team (the Safety Officers) are responsible for clarifying
 
 The Safety Team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
 
-Members of the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.
+Members of the Safety Team who violate the CoC will be required to recurse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.
 
 ## When and where does this Code of Conduct apply?
 
@@ -122,7 +122,7 @@ After you file a report, one or more members of our Safety Team will contact you
 
 All reports will be read and handled by the members of the Safety Team at sanger-tol.
 
-If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups.
+If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recurse themselves as per our Code of Conduct and will not have access to any follow-ups.
 
 To keep this first report confidential from any of the Safety Team members, please submit your first report by direct email to any of the safety officers you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with.
 

README.md

@@ -54,7 +54,7 @@ docker compose up
 You should then be able to access the website in your browser at [http://localhost:8888/](http://localhost:8888/).
 
 If you prefer, you can also use a tool such as [MAMP](https://www.mamp.info/) - if so,
-set the base directory to `/path/to/nf-co.re/public_html` in _Preferences > Web-Server > Document Root_ and then hit _Start Servers_.
+set the base directory to `/path/to/pipelines-website/public_html` in _Preferences > Web-Server > Document Root_ and then hit _Start Servers_.
 
 Most of the hand-written text is in `/markdown`, to make it easier to write. The PHP files in `/public_html` then parse this into HTML dynamically, if supplied with a filename.
 
@@ -160,11 +160,12 @@ If you are looking forward to contribute to the website or add your institution
 
 ## Community
 
-If you have any questions or issues, please [let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=priyanka-surana%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
+If you have any questions or issues, please [let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
 
 ## Credits
 
-Priyanka Surana ([@priyanka-surana](http://github.com/priyanka-surana/)) manages the content and Guoying Qi ([@gq1](https://github.com/gq1)) manages the website. Many individuals, especially Matthieu Muffato ([@muffato](http://github.com/muffato)), have made various contributions.
+Matthieu Muffato ([@muffato](http://github.com/muffato)) manages the content and Guoying Qi ([@gq1](https://github.com/gq1)) manages the website.
+Many individuals, especially Priyanka Surana ([@priyanka-surana](http://github.com/priyanka-surana/)), have made various contributions.
 
 Phil Ewels ([@ewels](http://github.com/ewels/)) built the original nf-core website.
 More recently, [@mashehu](https://github.com/mashehu) has done a great deal of work with the code.

composer.json

@@ -1,6 +1,6 @@
 {
- "name": "nf-core/nf-co.re",
- "description": "PHP dependencies for the main nf-core website.",
+ "name": "sanger-tol/pipelines-website",
+ "description": "PHP dependencies for the sanger-tol pipelines website.",
  "require": {
  "abraham/twitteroauth": "^2.0",
  "spatie/calendar-links": "1.8",

includes/footer.php

@@ -86,43 +86,35 @@
 
  </div>
  <div class="col-sm-6 col-lg-3 offset-lg-1 mb-3 d-print-none">
- <h5>Getting Started</h5>
+ <h5>Our documentation</h5>
  <ul class="list-unstyled">
- <li><a href="/pipelines">Available pipelines</a></li>
- <li><a href="/modules">nf-core modules</a></li>
- <li><a href="https://nf-co.re/tools">nf-core tools</a></li>
- <li><a href="https://nf-co.re/docs/usage/introduction">Getting started</a></li>
- <li><a href="https://nf-co.re/docs/usage/installation">Installation</a></li>
- <li><a href="https://nf-co.re/docs/usage/configuration">Pipeline configuration</a></li>
- <li><a href="https://nf-co.re/docs/usage/offline">Running offline</a></li>
- <li><a href="https://nf-co.re/docs/usage/tutorials">Usage tutorials</a></li>
- <li><a href="https://nf-co.re/docs/usage/data_management">Data Management</a></li>
- <li><a href="https://nf-co.re/docs/usage/troubleshooting">Troubleshooting</a></li>
- <li><a href="https://nf-co.re/docs/usage/tutorials/nextflow">Nextflow resources</a></li>
+ <li><a href="/pipelines">Pipelines</a></li>
+ <li><a href="/tools">Tools</a></li>
+ <li><a href="/docs/contributing/modules">Modules</a></li>
+ <li><a href="/docs/contributing/review_checklist">Code review</a></li>
  </ul>
  </div>
  <div class="col-sm-6 col-lg-3 mb-3 d-print-none">
- <h5>For Authors</h5>
+ <h5>nf-core documentation</h5>
  <ul class="list-unstyled">
- <li><a href="https://nf-co.re/docs/contributing/modules">DSL2 modules</a></li>
- <li><a href="https://nf-co.re/docs/contributing/subworkflows">DSL2 subworkflows</a></li>
- <li><a href="https://nf-co.re/docs/contributing/training_guide">Training guide</a></li>
- <li><a href="https://nf-co.re/docs/contributing/sync">Template synchronisation</a></li>
- <li><a href="https://nf-co.re/docs/contributing/tutorials">Developer tutorials</a></li>
- <li><a href="https://nf-co.re/docs/contributing/editor_plugins">Code editor plugins</a></li>
- <li><a href="https://nf-co.re/docs/contributing/design_guidelines">Graphic design guidelines</a></li>
+ <li><a href="https://nf-co.re/docs/usage/introduction">Getting started</a></li>
+ <li><a href="https://nf-co.re/docs/usage/installation">Installation</a></li>
+ <li><a href="https://nf-co.re/docs/usage/tutorials">Usage tutorials</a></li>
+ <li><a href="https://nf-co.re/docs/usage/tutorials/nextflow">Nextflow resources</a></li>
+ <li><a href="https://nf-co.re/tools">Command-line tool</a></li>
+ <li><a href="https://nf-co.re/modules">Modules</a></li>
  </ul>
  </div>
  <div class="col-sm-6 col-lg-2 mb-3 d-print-none">
- <h5>About sanger-tol</h5>
+ <h5>More information</h5>
  <ul class="list-unstyled">
  <li><a href="/about">About sanger-tol</a></li>
  <li><a href="/events">Events</a></li>
  <li><a href="/community">Community</a></li>
  <li><a href="/stats">Statistics</a></li>
  <li><a href="/publications">Publications</a></li>
  <li><a href="/code_of_conduct">Code of conduct</a></li>
- <li><a href="/join" class="mt-1 btn btn-outline-success">Join sanger-tol</a></li>
+ <li><a href="/connect" class="mt-1 btn btn-outline-success">Connect with sanger-tol</a></li>
  </ul>
  </div>
  </div>

includes/header.php

@@ -135,34 +135,24 @@ function gtag() {
  </button>
  <div class="collapse navbar-collapse justify-content-md-center" id="navbarCollapse">
  <ul class="navbar-nav">
- 
+
  <li class="nav-item p-1">
  <a class="nav-link" href="/">Home</a>
  </li>
 
+ <li class="nav-item p-1">
+ <a class="nav-link" href="/pipelines">Pipelines</a>
+ </li>
+
  <li class="nav-item p-1 dropdown">
- <a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Teams</a>
- <div class="dropdown-menu">
- <a class="dropdown-item" href="/it">Informatics Infrastructure (IT)</a>
- </div>
- </li>
-
- <li class="nav-item p-1 dropdown">
- <a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Projects</a>
+ <a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Resources</a>
  <div class="dropdown-menu">
  <a class="dropdown-item" href="/genome_after_party">Genome After Party</a>
+ <a class="dropdown-item" href="/tools">Tools</a>
  </div>
  </li>
-
- <li class="nav-item p-1">
- <a class="nav-link" href="/pipelines">Pipelines</a>
- </li>
-
- <li class="nav-item p-1">
- <a class="nav-link" href="/tools/">Tools</a>
- </li>
 
-  <li class="nav-item p-1">
+ <li class="nav-item p-1">
  <a class="nav-link" href="/docs">Docs</a>
  </li>
 
@@ -183,18 +173,18 @@ function gtag() {
  <a class="dropdown-item" href="/stats">Statistics</a>
  <a class="dropdown-item" href="/publications">Publications</a>
  <a class="dropdown-item" href="/code_of_conduct">Code of conduct</a>
- <a class="dropdown-item" href="/join">Join sanger-tol</a>
+ <a class="dropdown-item" href="/connect">Connect with sanger-tol</a>
  </div>
  </li>
 
  </ul>
 
  <hr class="d-md-none">
- <a class="d-md-none btn d-block btn-success mb-3" href="/join">
- Join sanger-tol
+ <a class="d-md-none btn d-block btn-success mb-3" href="/connect">
+ Connect with sanger-tol
  </a>
- <a class="d-none d-lg-block btn btn-success" style="position:absolute; right: 1rem;" href="/join">
- Join sanger-tol
+ <a class="d-none d-lg-block btn btn-success" style="position:absolute; right: 1rem;" href="/connect">
+ Connect with sanger-tol
  </a>
 
  </div>
@@ -208,7 +198,7 @@ function gtag() {
  <div class="container">
  <?php
  if (isset($md_github_url) and $md_github_url) {
- $md_github_url = str_replace('/docs/contributing/', '/developers/', $md_github_url);
+ $md_github_url = str_replace('/docs/contributing/', '/contributing/', $md_github_url);
  $md_github_url = str_replace('/docs/usage/', '/usage/', $md_github_url);
  echo '<a href="' .
  $md_github_url .

includes/module_page/_index.php

@@ -22,7 +22,7 @@
  }
 }
 mysqli_close($conn);
-// function to create bootstrap row with the first column for the name and type and the second for the descritption
+// function to create bootstrap row with the first column for the name and type and the second for the description
 function create_row($name, $type, $description, $pattern) {
  $id = strtolower(preg_replace('/[^\w\-\.]+/', '', str_replace(' ', '-', $name)));
  $id = str_replace('.', '-', $id); // periods break the js code, because they are not valid in selector ids

includes/pipeline_page/sidebar.php

@@ -71,7 +71,7 @@
  <button class="nav-link text-muted" id="nf-tab" data-bs-toggle="tab" data-bs-target="#nf" type="button" role="tab" aria-controls="nf" aria-selected="false">Nextflow</button>
  </li>
  <li class="nav-item" role="presentation">
- <button class="nav-link text-muted" id="tw-tab" data-bs-toggle="tab" data-bs-target="#tw" type="button" role="tab" aria-controls="tw" aria-selected="false">Tower</button>
+ <button class="nav-link text-muted" id="tw-tab" data-bs-toggle="tab" data-bs-target="#tw" type="button" role="tab" aria-controls="tw" aria-selected="false">Seqera Platform</button>
  </li>
  </ul>
  <div class="tab-content mt-2">
@@ -91,10 +91,10 @@
  </div>
  <div class="tab-pane" id="tw" role="tabpanel" aria-labelledby="tw-tab">
  <div class=" input-group input-group-sm pipeline-run-cmd">
- <input type="text" class="form-control input-sm code rounded-0" id="pipeline-tw-run-cmd-text" data-autoselect="" value="tw launch https://nf-co.re/<?php echo $pipeline->name .
+ <input type="text" class="form-control input-sm code rounded-0" id="pipeline-tw-run-cmd-text" data-autoselect="" value="tw launch https://github.com/sanger-tol/<?php echo $pipeline->name .
  $release_cmd; ?>" aria-label="Copy run command" readonly="">
  <button class="btn btn-outline-secondary copy-txt rounded-0" data-bs-target="pipeline-tw-run-cmd-text" data-bs-toggle="tooltip" data-bs-placement="left" title="Copy to clipboard" type="button"><i class="fas fa-clipboard px-1"></i></button>
- </div><p class="text-muted">Read how to configure the Tower CLI <u><a href='https://github.com/seqeralabs/tower-cli/#2-configuration' target="_blank">here</a></u>.</p></div>
+ </div><p class="text-muted">Read how to configure the Seqera Platform CLI <u><a href='https://github.com/seqeralabs/tower-cli/#2-configuration' target="_blank">here</a></u>.</p></div>
  </div>
  </div>
  </div>

includes/search_results.php

@@ -4,7 +4,7 @@
 require '../vendor/autoload.php';
 use Spyc;
 
-// $search_term - should be availble from include
+// $search_term - should be available from include
 $search_results = [
  'pipelines' => [],
  'documentation' => [],